The best way to use custom flags is to do as described in the documentation:

Can I use my own flags for the language switcher ?
Yes. You have to use PNG or JPG files and name them with the WordPress locale. For example, en_US.png. Then upload these files in the /wp­content/polylang/ directory (create the directory if it does not exist). Don't use the /polylang/flags/ directory as your files would be removed when automatically updating the plugin.

This modifies only the flags of the language switcher, not on the admin side.